Evaluate gene sets by cell type-specific gene expression
Wei Sun
2024-07-04
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 16.00 20.00 20.00 20.18 21.00 22.00## [1] 40## [1] 16 18 19 19 19 19 19 19 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
## [26] 20 21 21 21 21 21 21 21 21 21 22 22 22 22 22Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"##
## FALSE TRUE
## 1951 49##
## FALSE TRUE <NA>
## 45 1906 49gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ADPRHL2 ADPRS
## 2: AES TLE5
## 3: C12orf45 NOPCHAP1
## 4: C3orf58 DIPK2A
## 5: C6orf99 LINC02901
## 6: CBWD2 ZNG1B
## 7: CXorf57 RADX
## 8: FAM102A EEIG1
## 9: FAM122C PABIR3
## 10: FAM153C FAM153CP
## 11: FAM160A2 FHIP1B
## 12: GRASP TAMALIN
## 13: H2AFX H2AX
## 14: HIST1H2AG H2AC11
## 15: HIST1H2BC H2BC5
## 16: HIST1H2BK H2BC12
## 17: HIST1H2BN H2BC15
## 18: HIST1H3A H3C1
## 19: HIST1H3H H3C10
## 20: HIST1H4C H4C3
## 21: HIST2H2BF H2BC18
## 22: LRMP IRAG2
## 23: MFSD14C MFSD14CP
## 24: MKL1 MRTFA
## 25: MPP6 MPHOSPH6
## 26: RNASEH1-AS1 RNASEH1-DT
## 27: SEPT6 SEPTIN6
## 28: SEPT9 SEPTIN9
## 29: TMEM161B-AS1 TMEM161B-DT
## 30: ARNTL BMAL1
## 31: C6orf106 ILRUN
## 32: C6orf203 MTRES1
## 33: FAM129A NIBAN1
## 34: FAM160B1 FHIP2A
## 35: FAM192A PSME3IP1
## 36: HEXDC HEXD
## 37: HIST1H1E H1-4
## 38: KIAA0100 BLTP2
## 39: KIAA1551 RESF1
## 40: LARS LARS1
## 41: MARS MARS1
## 42: PLA2G16 PLAAT3
## 43: SEPT2 SEPTIN6
## 44: SMIM37 MTLN
## 45: YARS YARS1
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3## sym_in_data sym_limma gene_symbol
## 1: ABCD3 ABCD3 ABCD3
## 2: ABCG1 ABCG1 ABCG1
## 3: ABHD5 ABHD5 ABHD5
## 4: ABI1 ABI1 ABI1
## 5: ABLIM1 ABLIM1 ABLIM1## t1
## 1 2
## 1998 1## sym_in_data sym_limma gene_symbol
## 1: SEPT6 SEPTIN6 SEPTIN6
## 2: SEPT2 SEPTIN6 SEPTIN6Read in cell type-specific expression data
Cell type specific gene expression were downloaded from protein atlas.
## [1] 1587110 4## Gene Gene name Cell type nTPM
## 1: ENSG00000000003 TSPAN6 Adipocytes 149.5
## 2: ENSG00000000003 TSPAN6 Alveolar cells type 1 6.1
## 3: ENSG00000000003 TSPAN6 Alveolar cells type 2 10.5
## 4: ENSG00000000003 TSPAN6 Astrocytes 13.9
## 5: ENSG00000000003 TSPAN6 B-cells 1.5## [1] 79##
## Adipocytes Alveolar cells type 1
## 20090 20090
## Alveolar cells type 2 Astrocytes
## 20090 20090
## B-cells Basal keratinocytes
## 20090 20090
## Basal prostatic cells Basal respiratory cells
## 20090 20090
## Basal squamous epithelial cells Bipolar cells
## 20090 20090
## Breast glandular cells Breast myoepithelial cells
## 20090 20090
## Cardiomyocytes Cholangiocytes
## 20090 20090
## Club cells Collecting duct cells
## 20090 20090
## Cone photoreceptor cells Cytotrophoblasts
## 20090 20090
## dendritic cells Distal enterocytes
## 20090 20090
## Distal tubular cells Ductal cells
## 20090 20090
## Early spermatids Endometrial ciliated cells
## 20090 20090
## Endometrial stromal cells Endothelial cells
## 20090 20090
## Enteroendocrine cells Erythroid cells
## 20090 20090
## Excitatory neurons Exocrine glandular cells
## 20090 20090
## Extravillous trophoblasts Fibroblasts
## 20090 20090
## Gastric mucus-secreting cells Glandular and luminal cells
## 20090 20090
## granulocytes Granulosa cells
## 20090 20090
## Hepatocytes Hofbauer cells
## 20090 20090
## Horizontal cells Inhibitory neurons
## 20090 20090
## Intestinal goblet cells Ionocytes
## 20090 20090
## Kupffer cells Langerhans cells
## 20090 20090
## Late spermatids Leydig cells
## 20090 20090
## Macrophages Melanocytes
## 20090 20090
## Microglial cells monocytes
## 20090 20090
## Mucus glandular cells Muller glia cells
## 20090 20090
## NK-cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Pancreatic endocrine cells
## 20090 20090
## Paneth cells Peritubular cells
## 20090 20090
## Plasma cells Prostatic glandular cells
## 20090 20090
## Proximal enterocytes Proximal tubular cells
## 20090 20090
## Respiratory ciliated cells Rod photoreceptor cells
## 20090 20090
## Salivary duct cells Schwann cells
## 20090 20090
## Serous glandular cells Sertoli cells
## 20090 20090
## Skeletal myocytes Smooth muscle cells
## 20090 20090
## Spermatocytes Spermatogonia
## 20090 20090
## Squamous epithelial cells Suprabasal keratinocytes
## 20090 20090
## Syncytiotrophoblasts T-cells
## 20090 20090
## Theca cells Thymic epithelial cells
## 20090 20090
## Undifferentiated cells
## 20090## [1] 602700 5## Gene Gene name Immune cell TPM pTPM
## 1: ENSG00000000003 TSPAN6 basophil NA 1.2
## 2: ENSG00000000003 TSPAN6 Central memory CD8 T-cell NA 1.7
## 3: ENSG00000000003 TSPAN6 classical monocyte NA 0.2
## 4: ENSG00000000003 TSPAN6 Effector memory CD8 T-cell NA 0.7
## 5: ENSG00000000003 TSPAN6 Exhausted memory B-cell NA 0.7## Mode NA's
## logical 602700## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 0.00 3.10 49.74 27.20 96572.50## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.10 1.70 11.60 67.96 42.80 96572.50## [1] 30##
## basophil Central memory CD8 T-cell
## 20090 20090
## classical monocyte Effector memory CD8 T-cell
## 20090 20090
## Exhausted memory B-cell intermediate monocyte
## 20090 20090
## MAIT T-cell Memory CD4 T-cell TFH
## 20090 20090
## Memory CD4 T-cell Th1 Memory CD4 T-cell Th1/Th17
## 20090 20090
## Memory CD4 T-cell Th17 Memory CD4 T-cell Th2
## 20090 20090
## myeloid DC naive B-cell
## 20090 20090
## naive CD4 T-cell naive CD8 T-cell
## 20090 20090
## neutrophil NK-cell
## 20090 20090
## non-classical monocyte Non-switched memory B-cell
## 20090 20090
## Non-Vd2 gdTCR Plasmablast
## 20090 20090
## plasmacytoid DC Progenitor cell
## 20090 20090
## Switched memory B-cell T-reg
## 20090 20090
## Terminal effector memory CD4 T-cell Terminal effector memory CD8 T-cell
## 20090 20090
## total PBMC Vd2 gdTCR
## 20090 20090## [1] 30 2## Cell_type Lineage
## 1: Basophil Granulocytes
## 2: Neutrophil GranulocytesCheck gene expression for each gene set
## [1] 2000 3for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]
n_genes = sum(genes %in% ct_immune$`Gene name`)
print(sprintf("found %d genes.", n_genes))
if(n_genes == 0) { next }
df = ct_immune[`Gene name` %in% genes,]
dim(df)
df[1:2,]
stopifnot(all(str_to_lower(df$`Immune cell`) %in%
str_to_lower(lineage$Cell_type)))
mat1 = match(str_to_lower(df$`Immune cell`),
str_to_lower(lineage$Cell_type))
df = cbind(df, lineage[mat1,])
df[1:2,]
df$Cell_type = factor(df$Cell_type, levels = lineage$Cell_type)
df = df[df$Lineage != "Total PBMC",]
df$Lineage = factor(df$Lineage,
levels = setdiff(lineage$Lineage, "Total PBMC"))
p1 = ggplot(df, aes(x=Cell_type, y=log10(pTPM + 0.1), fill=Lineage)) +
geom_boxplot() + xlab("Cell type") + ggtitle(set_k) +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
scale_fill_brewer(palette="RdBu")
print(p1)
}## [1] 1
## [1] "CHD2" "ENOSF1" "GRASP" "JPX" "PHYH" "TBCCD1"
## [7] "TCTA" "YPEL2" "ZNF831" "ABHD2" "ERICH1" "GNPAT"
## [13] "IRAK4" "MORC3" "NLRC5" "ODF3B" "PEX11B" "SEC14L1"
## [19] "TNFRSF18" "ZBP1" "ZNF236"
## [1] "found 20 genes."
## [1] 2
## [1] "ARHGAP9" "ARID4A" "CCM2" "CD96" "CITED2" "DGKA"
## [7] "HELQ" "HIST1H3H" "IFRD1" "ING2" "MXD1" "RCAN3"
## [13] "RGCC" "RIC1" "SLC12A7" "SLC8B1" "STARD10" "TESPA1"
## [19] "TMEM204" "WARS2"
## [1] "found 20 genes."
## [1] 3
## [1] "AC093323.1" "AC245297.3" "ERVK3-1" "FAM122C" "GPCPD1"
## [6] "LINC01215" "LINC02265" "MAP3K2" "MDS2" "PLCL1"
## [11] "SLC25A32" "ST7L" "TBPL1" "TRAV38-2DV8" "TRBV5-4"
## [16] "TRBV6-6" "TRBV7-3" "TTC3" "ZNF506" "MIR4435-2HG"
## [21] "PMVK"
## [1] "found 15 genes."
## [1] 4
## [1] "AC007952.4" "AC025164.1" "AC087239.1" "ATP2B1-AS1" "CD82"
## [6] "CSKMT" "IER2" "ILF3-DT" "LBH" "LINC00861"
## [11] "NPIPB4" "NUP58" "PPP1R15A" "PRR7" "SLC2A3"
## [16] "TAGAP" "WHAMM" "Z93241.1" "AZI2" "CCDC43"
## [21] "ITGAL" "N4BP1"
## [1] "found 15 genes."
## [1] 5
## [1] "CCDC66" "CDC42SE2" "CEP95" "EPHB6" "FHIT" "FOXN3"
## [7] "HIST1H2BC" "NR4A3" "NSUN6" "PIK3IP1" "PLK3" "RSRP1"
## [13] "SENP7" "SLC44A1" "WSB1" "ZFP36L1" "ITK" "RECK"
## [19] "SAMD9"
## [1] "found 19 genes."
## [1] 6
## [1] "ABHD5" "AC119396.1" "AC245014.3" "AL133415.1" "AL139246.5"
## [6] "ARL4A" "ATG9B" "FBXO3" "IL23A" "LTB"
## [11] "MCUB" "MHENCR" "NAA16" "NOP53" "POLD4"
## [16] "SCML4" "SLC25A38" "SNRK" "TBCC" "TNFRSF25"
## [21] "ZC3H12D"
## [1] "found 16 genes."
## [1] 7
## [1] "COQ7" "IER3" "MZF1" "ADGRE5" "ARL4C" "C1orf21" "CFD"
## [8] "CST7" "CX3CR1" "DIAPH2" "ETNK1" "GZMM" "MCTP2" "NCBP3"
## [15] "PLEK" "PPP2R5B" "PTGDR" "PTPN7" "RNPEPL1" "TTC16"
## [1] "found 20 genes."
## [1] 8
## [1] "AC008105.3" "AC025171.2" "ADA2" "AK5" "ARRDC2"
## [6] "CHRM3-AS2" "DNASE1" "GSTM4" "KLF7" "NRIP1"
## [11] "NUAK2" "PDE7A" "RNASEH1-AS1" "SLC22A17" "TUBD1"
## [16] "TUBE1" "ZNF84" "ZNF862" "SPTLC2" "TMEM62"
## [1] "found 16 genes."
## [1] 9
## [1] "ANKH" "CSRNP1" "DHRS3" "EPHX2" "KANSL2" "OXLD1"
## [7] "PECAM1" "ZNF10" "C12orf75" "GON4L" "IL4R" "INPP5D"
## [13] "KMT2B" "NARF" "PHF20" "PHF20L1" "SP140" "TNFRSF4"
## [1] "found 18 genes."
## [1] 10
## [1] "MFSD14C" "STARD7" "WAPL" "ABHD3" "AC016831.7"
## [6] "AC022916.1" "AC118549.1" "CARMIL2" "EAPP" "ECPAS"
## [11] "KANSL1-AS1" "NRDC" "PARP11" "PUM3" "RAPGEF1"
## [16] "SLC20A2" "SPATA13" "TM2D1" "UTP25" "Z93930.2"
## [1] "found 14 genes."
## [1] 11
## [1] "BCL3" "C20orf204" "DDX3Y" "EIF1AY" "FAAH2" "HRH2"
## [7] "KDM5D" "OSM" "PCSK1N" "RPS4Y1" "S100A12" "SLF2"
## [13] "SOCS3" "TTTY15" "UTY" "ZFYVE28"
## [1] "found 15 genes."
## [1] 12
## [1] "AC145124.1" "AIF1" "AKIRIN1" "BOLA2-SMG1P6" "C12orf45"
## [6] "COQ10B" "CRLF3" "IL16" "LINC01550" "MMP28"
## [11] "MYNN" "NUDT4" "OSER1" "OTULINL" "PECR"
## [16] "TMEM161B-AS1" "TMEM71" "YY1AP1" "JAKMIP1" "SERTAD3"
## [21] "SUSD6" "TMEM138"
## [1] "found 18 genes."
## [1] 13
## [1] "DELE1" "DSE" "GIMAP1" "IER5" "KLRB1" "PITPNC1"
## [7] "RAB37" "SLC25A33" "SNX18" "TBC1D10C" "TRBC2" "TTC31"
## [13] "UCP2" "APOBEC3G" "GNPTAB" "GZMB" "KLRG1" "LAG3"
## [19] "MATK" "SMPD2"
## [1] "found 20 genes."
## [1] 14
## [1] "ERCC5" "FAM8A1" "BROX" "CCDC88B" "CD320" "CISH" "CTBS"
## [8] "FKBP11" "IL2RB" "IL2RG" "KCNAB2" "PRDM1" "PREP" "PVT1"
## [15] "REXO2" "RNMT" "STAT4" "TGS1" "TSHZ2" "UGCG"
## [1] "found 19 genes."
## [1] 15
## [1] "AC084033.3" "AMD1" "CAMK4" "CCDC141" "CXorf57"
## [6] "EVI2B" "FAM102A" "FAM117B" "FYB1" "INPP4B"
## [11] "IPCEF1" "MAML2" "MTRNR2L12" "SNHG12" "TC2N"
## [16] "TMC8" "TMEM107" "TSC22D2" "ADAM19" "SCAMP4"
## [21] "ZNF292"
## [1] "found 18 genes."
## [1] 16
## [1] "ATAD1" "BTN3A1" "CHMP1B" "CHMP7" "COG5" "DBP"
## [7] "DIP2B" "LRRC8D" "NSMAF" "PARP16" "PCNP" "PPP1R15B"
## [13] "SPIDR" "STX16" "THAP6" "TMEM245" "TSPYL4" "ZBTB25"
## [19] "ZMAT1" "BTN3A2" "NEK9" "TAOK3"
## [1] "found 22 genes."
## [1] 17
## [1] "AC016405.3" "AC020911.2" "AC025171.3" "AC091271.1" "AC103591.3"
## [6] "AF213884.3" "AL121944.1" "AL357060.1" "AL451085.1" "C6orf99"
## [11] "ID3" "JAML" "KLF12" "LINC01465" "LRRN3"
## [16] "OSER1-DT" "PARP8" "PNISR" "CNOT4" "SDF2"
## [21] "WDR7"
## [1] "found 9 genes."
## [1] 18
## [1] "AL627171.1" "NDUFV2-AS1" "ZNF490" "ADTRP" "ATAD2B"
## [6] "CEMIP2" "CRYBG1" "GRK2" "IGLV3-25" "KIAA0040"
## [11] "LRRC58" "MT1X" "NORAD" "SLFN12L" "SNHG9"
## [16] "TENT5C" "THUMPD3-AS1" "TRBV6-1" "UBALD2" "VPS13D"
## [1] "found 15 genes."
## [1] 19
## [1] "CLK4" "MYADM" "ZNF821" "BLOC1S6" "C2orf68" "CD7" "CLASRP"
## [8] "IFNAR1" "KLF9" "NME3" "P4HTM" "PIK3CB" "PIM2" "PRMT2"
## [15] "RNF145" "SACS" "SETD5" "SLC35A2" "SNX9" "SP140L"
## [1] "found 20 genes."
## [1] 20
## [1] "AC025159.1" "AL135791.1" "CERNA1" "LDLRAP1" "LINC02273"
## [6] "LRRC8C-DT" "LYRM9" "NSMCE3" "PITPNA-AS1" "SNHG7"
## [11] "TSPOAP1-AS1" "AC020915.3" "GPR132" "HACD3" "MFSD14A"
## [16] "NNT-AS1" "NSD3" "TOMM70" "TSPAN14" "TUT4"
## [1] "found 10 genes."
## [1] 21
## [1] "ADK" "ARL6IP1" "C6orf62" "EFCAB2" "HEATR5B" "MBD6" "MTERF4"
## [8] "ST3GAL1" "STMN3" "TOB2" "TPP2" "EHMT1" "FRY" "FRYL"
## [15] "ICE1" "SDR39U1" "SYNRG" "UBA7" "UBE3B" "VPS36"
## [1] "found 20 genes."
## [1] 22
## [1] "CBLL1" "CST3" "FAM118A" "FCN1" "GIMAP8" "IGKV1-5"
## [7] "IGLV1-44" "NT5DC1" "PYROXD1" "RABL2B" "ALOX5AP" "GAB3"
## [13] "IFI44" "KIAA1551" "MX2" "OAS2" "PPP2R3C" "SRP54"
## [19] "STK10"
## [1] "found 19 genes."
## [1] 23
## [1] "RBKS" "SUPT20H" "AC116407.2" "APOL6" "ARHGEF3"
## [6] "ATXN7L3B" "C4orf48" "CARD16" "ENY2" "GIMAP7"
## [11] "LPIN1" "LPIN2" "MESD" "PDE4B" "PHPT1"
## [16] "PTGER2" "RCBTB2" "RNF19A" "TCAF2" "TMEM156"
## [1] "found 18 genes."
## [1] 24
## [1] "AL118516.1" "KIF9" "RGS10" "UPF3A" "BUD23"
## [6] "CD69" "CYTIP" "DDIT4" "EFR3A" "GIMAP4"
## [11] "IFITM2" "ISG20" "KLF6" "MTRNR2L8" "NAA38"
## [16] "NADSYN1" "NBDY" "SIGIRR" "SMIM37" "STK17B"
## [1] "found 19 genes."
## [1] 25
## [1] "CD38" "IGLV2-14" "KIAA1328" "MBNL2" "RPS26" "SIMC1"
## [7] "XIST" "APOL1" "CCL5" "CCR4" "GZMA" "LINC01871"
## [13] "MYO1G" "RAP1GAP2" "RSAD2" "SAMD9L" "SPON2" "TGFBR3"
## [19] "VCAN"
## [1] "found 17 genes."
## [1] 26
## [1] "NFYB" "PHC1" "ANK3" "ARID5B" "CCDC12" "CREBZF" "GCN1"
## [8] "IL32" "NFE2L1" "NQO2" "NT5C" "PCGF5" "PLAC8" "SYTL1"
## [15] "TIPARP" "TMED4" "XBP1" "ZDHHC20" "ZNF593"
## [1] "found 19 genes."
## [1] 27
## [1] "AC009061.2" "AL645728.1" "AP002360.1" "C12orf29" "COX10"
## [6] "FBXO8" "GIMAP6" "HDHD2" "IL6R" "KLHL6"
## [11] "LST1" "MAST4" "NBPF14" "OTUD5" "RETREG1"
## [16] "SMDT1" "TBCK" "TRAV8-6" "ZFP14" "BISPR"
## [21] "C12orf4" "PARP4"
## [1] "found 18 genes."
## [1] 28
## [1] "CD28" "KLF10" "ODC1" "SH3YL1" "AGAP2" "AP3M2" "AREG"
## [8] "CRIP2" "CRTC3" "EDA" "GABPB2" "ICOS" "IL21R" "KHNYN"
## [15] "LTBP3" "LY96" "NFKBIZ" "PLEKHA2" "SMAD5" "TOB1" "ZNF101"
## [1] "found 21 genes."
## [1] 29
## [1] "C16orf74" "C1GALT1" "COQ8A" "CTSF" "FCMR" "HIVEP2"
## [7] "LEPROT" "LIMD2" "LIPT1" "MLXIP" "ORC4" "PCMTD2"
## [13] "RASA2" "SPART" "TBC1D7" "TMEM154" "TRABD2A" "TRAV23DV6"
## [19] "ZNF140" "NDUFC1" "TMEM175"
## [1] "found 21 genes."
## [1] 30
## [1] "DPEP2" "FAM227B" "GGT7" "MAP3K8" "ZFX" "ASCL2" "B3GALT4"
## [8] "CCDC112" "CD58" "FAM129A" "GALNS" "IFIT1" "IFIT2" "IFIT3"
## [15] "NBEAL2" "NRROS" "PHF23" "POGLUT1" "ZEB2" "ZNF276"
## [1] "found 20 genes."
## [1] 31
## [1] "RNASEK" "ARHGAP10" "BCL9L" "CARD11" "CMIP" "CROT"
## [7] "DENND4B" "EIF2AK4" "GPRIN3" "IFI35" "KIF21A" "KIF21B"
## [13] "KLHDC4" "LY6E" "PLA2G16" "PRDM2" "PREX1" "SBNO2"
## [19] "SCAF8" "SLA"
## [1] "found 20 genes."
## [1] 32
## [1] "AC004687.1" "AC027644.3" "AC097376.2" "AL359220.1" "CASP4"
## [6] "COQ10A" "GOLGA8B" "GZMK" "KCNK6" "MATR3-1"
## [11] "MUC20-OT1" "RGS1" "TRAV12-2" "TRAV25" "TRAV41"
## [16] "TRBV6-5" "WASHC4" "ZNF600" "ZNF91" "FRMD4B"
## [21] "SPOCK2"
## [1] "found 15 genes."
## [1] 33
## [1] "ACADSB" "C3orf58" "COL18A1" "DAPP1" "FAM153C" "INTS6"
## [7] "IP6K2" "MYLIP" "NABP1" "NEK1" "NR1D1" "NR1D2"
## [13] "PLEKHM1" "RCSD1" "SLC26A11" "TECPR1" "DOCK11" "LPCAT4"
## [19] "PPRC1"
## [1] "found 18 genes."
## [1] 34
## [1] "BTG1" "BTG2" "C1orf43" "EGR1" "FBXL3" "LCLAT1" "TCF7"
## [8] "ATP8B2" "CHD6" "ETV6" "FBXO9" "IFNGR2" "KIF3B" "NEAT1"
## [15] "PCED1B" "PIEZO1" "RHOH" "TBC1D14" "ZNF708"
## [1] "found 18 genes."
## [1] 35
## [1] "ODF2L" "UTP6" "YPEL5" "ANKAR" "DTX3L" "FAM53B" "GBP1" "GBP3"
## [9] "GBP5" "GNLY" "HSH2D" "IFI44L" "IRF1" "IRF9" "MX1" "MYO1F"
## [17] "NKG7" "PARP14" "PARP9" "XAF1"
## [1] "found 20 genes."
## [1] 36
## [1] "AC013264.1" "ACSS1" "AL138963.3" "ANXA2R" "C7orf31"
## [6] "CFAP36" "LINC00623" "METAP1" "METTL21A" "SNHG8"
## [11] "SP3" "STK19" "TRAV12-1" "TRAV13-2" "TRAV21"
## [16] "TRAV8-3" "TRAV9-2" "TRBV28" "TRBV6-2" "ZFAS1"
## [21] "ZNF749" "C1orf162"
## [1] "found 17 genes."
## [1] 37
## [1] "ARHGAP15" "ATG13" "CD40LG" "DPYD" "ERAP2" "HOXB2"
## [7] "IGKV3-20" "LAX1" "SGSM3" "SLC7A6" "TCP11L2" "TGIF1"
## [13] "TRAV14DV4" "TRBC1" "TTC39C" "UBL3" "XRRA1" "CARD8-AS1"
## [19] "MT2A" "OAS1"
## [1] "found 19 genes."
## [1] 38
## [1] "AC004854.2" "AC015982.1" "AC023157.3" "AC083880.1" "AC087623.3"
## [6] "ARF4-AS1" "BX284668.6" "HIPK1-AS1" "JCHAIN" "KCNQ1OT1"
## [11] "LETM2" "LINC00649" "MZF1-AS1" "NOCT" "NPIPB11"
## [16] "NPIPB5" "PHLDA1" "SDR42E2" "THAP9-AS1" "TOX"
## [21] "MYBL1"
## [1] "found 9 genes."
## [1] 39
## [1] "ABCC10" "ADGRG1" "AKNA" "CCL4" "CD300A" "CTSW"
## [7] "FCRL6" "FGFBP2" "GPR65" "MIAT" "PAXX" "RASAL3"
## [13] "S1PR5" "TRANK1" "TRAV29DV5" "TRBV12-3" "TSPAN32" "TTC38"
## [19] "USP30-AS1" "ZNF683"
## [1] "found 18 genes."
## [1] 40
## [1] "ARMH1" "COA1" "LRMP" "RAB33B" "RNF139" "TRAV8-2"
## [7] "ZSCAN18" "APH1B" "CITED4" "COL6A3" "COX17" "HELB"
## [13] "RNF157" "RTKN2" "SESN3" "SLC23A2" "SLC25A37" "SLC9A8"
## [19] "TAF4B" "ZNF267"
## [1] "found 20 genes."
Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 4156999 222.1 11673970 623.5 NA 11673970 623.5
## Vcells 20567925 157.0 51369168 392.0 65536 51368243 392.0## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] stringr_1.5.0 limma_3.54.2 tidyr_1.3.0 ggpubr_0.6.0
## [5] ggplot2_3.4.2 data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.10 png_0.1-8 Biostrings_2.66.0
## [4] digest_0.6.31 utf8_1.2.3 R6_2.5.1
## [7] GenomeInfoDb_1.34.9 backports_1.4.1 stats4_4.2.3
## [10] RSQLite_2.3.1 evaluate_0.20 httr_1.4.6
## [13] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.0
## [16] rstudioapi_0.14 car_3.1-2 jquerylib_0.1.4
## [19] blob_1.2.4 R.oo_1.25.0 R.utils_2.12.2
## [22] S4Vectors_0.36.2 rmarkdown_2.21 labeling_0.4.2
## [25] RCurl_1.98-1.12 bit_4.0.5 munsell_0.5.0
## [28] broom_1.0.4 compiler_4.2.3 xfun_0.39
## [31] pkgconfig_2.0.3 BiocGenerics_0.44.0 htmltools_0.5.5
## [34] tidyselect_1.2.0 KEGGREST_1.38.0 GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1 IRanges_2.32.0 fansi_1.0.4
## [40] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0
## [43] R.methodsS3_1.8.2 bitops_1.0-7 grid_4.2.3
## [46] jsonlite_1.8.4 gtable_0.3.3 lifecycle_1.0.3
## [49] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
## [52] cli_3.6.1 stringi_1.7.12 cachem_1.0.7
## [55] carData_3.0-5 farver_2.1.1 XVector_0.38.0
## [58] ggsignif_0.6.4 bslib_0.4.2 generics_0.1.3
## [61] vctrs_0.6.2 RColorBrewer_1.1-3 org.Hs.eg.db_3.16.0
## [64] tools_4.2.3 bit64_4.0.5 Biobase_2.58.0
## [67] glue_1.6.2 purrr_1.0.1 abind_1.4-5
## [70] fastmap_1.1.1 yaml_2.3.7 AnnotationDbi_1.60.2
## [73] colorspace_2.1-0 rstatix_0.7.2 memoise_2.0.1
## [76] knitr_1.44 sass_0.4.5